Dna joining method

ABSTRACT

The present invention provides a method to directionally clone any linear template DNA molecule into any linearized vector. The vector ends may be generated from any restriction enzyme cleavage. The method does not require a ligation step nor the use of carefully controlled conditions as is required with methods involving specific exonucleases alone. It has been determined that specific DNA polymerases are able to efficiently join one or more linear DNA molecules sharing ends with appropriate complementation.

FIELD OF THE INVENTION

The present invention is in the field of recombinant DNA technology. Specifically, the present invention relates to a method of directionally joining one or more DNA molecules using a DNA polymerase, and the application of this method to the cloning of PCR products.

BACKGROUND OF THE INVENTION

The Polymerase Chain Reaction (PCR) (Mullis and Faloona 1987; Saiki, Gelfand et al. 1988) is an integral technique in scientific research. Cloning of PCR products is often an obligate step towards reaching a research objective. PCR-cloning presents numerous challenges and various techniques have been devised over the years to minimize its limitations. Cloning of PCR products generally fall into one of the following methodologies; i) traditional PCR-cloning using restriction enzymes and ligase, ii) T-vector or TA-cloning, iii) uracil DNA glycosylase (UDG)-based cloning iv) PCR-based techniques, v) in vivo recombinase methods, and vi) exonuclease-mediated cloning. Each of these methodologies is described below.

i) Traditional PCR-Cloning

Cloning of PCR-amplified DNA was traditionally facilitated by incorporating restriction endonuclease (RE) sites into the PCR primers, allowing for subsequent digestion of the PCR product with the appropriate enzyme followed by insertion into a compatible vector (Sharf et al., 1990). One problem often encountered with this method is that REs are notoriously poor cutters when their recognition sequences are close to the ends of the DNA substrate (Kaufman and Evans 1990). A second complication is that sequences within the PCR-amplified region can be lost if a second restriction site for the same RE is unknowingly present. This necessitates that the complete sequence of the PCR product be known prior to choosing which RE to use. Once the vector and DNA insert have been digested with the same RE, the two DNA molecules can be covalently joined by DNA ligase in a reaction typically taking 4-12 hr. It should be noted that during any ligation reaction, it is critical that the vector and insert are present in appropriate ratios, which is often difficult to determine. The reaction products are then used to transform competent E. coli cells. A subtle variation on this theme called “ligation by overlap extension” has been devised which does not require any subsequent ligation reaction, but does require two additional primers, and the entire vector sequence itself must be amplified (Shuldiner, Tanner et al. 1991).

Blunt-end cloning of PCR fragments has also been used extensively, although this technique is relatively inefficient because of the problems encountered by DNA ligase when joining together two blunt-ended DNA molecules. This technique is also complicated by the fact that Taq polymerase (the prototypical PCR amplifying enzyme) has a propensity for adding 3′ terminal adenine residues through its terminal transferase activity (Clark 1988; Mole, Iggo et al. 1989). Approximately 50% of all PCR products generated using Taq polymerase contain these 3′ extensions (Clark, 1988). One way around this problem is to “polish” or remove these added adenine residues with Klenow (Hemsley, Arnheim et al. 1989) or T4 DNA polymerase (Costa and Weiner 1994), adding an additional step to the protocol.

Recent discoveries of different thermostable polymerases including Pfu polymerase from Pyrococcus furiosis and Vent_(R) polymerase from the archaebacteria Thermococcus litoralis do not produce 3′ adenine residue extensions due to inherent 3′-5′ exonuclease activities. In addition to the problems produced by the amplifying polymerase, this technique does not allow for directional cloning, meaning that the orientation of insert in the recombinant DNA cannot be predetermined.

ii) T-Vector and TA-Cloning

The terminal transferase activity of Taq polymerase has been exploited by many researchers in a technique now commonly known as TA-cloning. The chosen vector is digested with the appropriate RE so as to yield ends with protruding thymidine residues, the natural complement to the 3′-overhanging adenosine residues found on the PCR-amplified DNA. The most significant drawback of this technique is that vectors must be specifically engineered to produce compatible ends. The only simple way of accomplishing this goal is to restrict the vector to produce blunt ends, and then treat it with Taq polymerase in the presence of only dTTP's. Numerous companies have developed kits based on this technique, including pCR-Script™ SK(S) kit from Stratagene, pGEM®-T from Promega, the SureClone™ ligation kit from Pharmacia and the pT7Blue T-vector kit from Novagen. The main limitation to these methods is that a vector supplied by the manufacturer must be used and a second subcloning step is often necessary to move the cloned DNA fragment into a vector of choice. An inexpensive alternative to buying these kits is to use a T-vector pGEM®-5fZ(+) which is available for little or no cost from the American Type Culture Collection (ATCC). This vector when digested with Xcm1 provides the T-overhangs used for TA-cloning (Kovalic, Kwak et al, 1991; Mead, Pey et al. 1991). Numerous other T-vectors have been developed independently (Cha. Bishai et al. 1993; Ichihara and Kurosawa 1993) which, after appropriate RE digestion, yield appropriate ends. Such vectors, however, required extensive manipulations to create. Some other potential problems with these kits have been reported recently (Hengen 1995). High backgrounds were observed for the pCR-Script vector when tested alone, PCRII contains a pBR322 origin of replication and thus replicate to low copy numbers, and repeated freeze-thaw cycles at −20° C. can lead to instability and loss of the T-tails. All the T-vector techniques suffer from the drawback that they are non-directional and require a ligation step.

Invitrogen have improved upon traditional TA-cloning by bypassing the need for a ligation step. This method, called TOPO TA-cloning, takes advantage of a reaction catalyzed by a vaccinia virus enzyme called topoisomerase I (Shuman, 1994 and U.S. Pat. No. 5,766,891). Topoisomerase can bind to double-stranded DNA and cleave the phosphodiester backbone in one of the duplex strands. The enzyme is sequence specific, cleaving primarily at the recognition sequence 5′-(C/T)CCTT↓-3′ (Shuman and Prescott 1990; Shuman 1991). The enzyme is capable of re-ligating the original strand back together, or ligating two heterologous DNAs in the formation of a recombinant species (Shuman 1992; Shuman 1992). The reaction is very efficient requiring only a 5 minute benchtop incubation. The methodology also has advantages which obviates the need for ligase, does not require knowledge of the entire insert sequence and no additional nucleotides need be added to PCR primers. However, only specific plasmids engineered to contain the TOPO recognition sequence can be used. These vectors are produced by restricting the vector followed by adding specific linkers or adaptors, which is not a trivial task. Another limitation of this technique, is that the TOPO recognition sequence must be located within 10 bp from the 3′-ends of the vector, and furthermore, the insert must have a 5-OH group. The issue has been raised that internal recognition sequences within the amplified DNA may result in complications, however these sites are simply religated and do not impose any restrictions on this technique (Shuman 1994; Stivers, Shuman et at. 1994). Under general use, the Invitrogen kit provided another potential problem (unpublished results). The traditional method for screening clones, called blue-white selection, does not produce definitive results with the Invitrogen kit. Therefore, it is necessary to assay both white and light-blue colonies to ensure the correct construct is obtained.

iii) Uracil DNA-Glycosylase (UDG)-Based Cloning

Rashtchian et al., (1992) developed a ligase independent PCR cloning method using uracil DNA glycosylase (UDG), an enzyme whose normal cellular role is a DNA repair enzyme. The technique requires a 12-hp addition (CUACUACUACUA) to the 5′ end of the PCR primers. The glycosylase selectively removes dUMP residues at the ends of the PCR products which disrupts proper base-pairing leading to single-strand 3′-overhangs (Duncan and Chambers 1984; Longo, Berninger et al. 1990). These 3′-overhangs can anneal to appropriately prepared single-strand ends of a vector. Uracil glycosylase is not active with thymine residues, the DNA counterpart of uracil residues (Duncan and Chambers, 1984), and is capable of removing dUMP residues even near the extreme ends (Varshney and van de Sande 1991). This methodology requires that the vector contain the appropriate complementary sequences, and is not amenable to use with proofreading polymerases such as Pfu or Vent_(R) polymerases (Sakaguchi, Sedlak et al. 1996). The researchers must therefore use Taq polymerase which has a significantly increased error frequency. UDG-based cloning has been commercialized by Life Technologies with their Clone Amp^(R) pUC system.

A variation on UDG-cloning takes advantage of the abasic sites (AP) produced by UDG-cleavage at dUMP residues. These AP sites are substrates for AP endonucleases such as T4 endonuclease V or human AP endonuclease I. Treatment with either of these repair enzymes yields a 5-P which is suitable for subsequent ligation into the appropriate vector. One drawback of this method is the requirement for a modified base (deoxyuridine) in the primer, and success relies on two enzymes in addition to ligase treatment. A second more obscure variation of UDG-cloning involves the use of a non-base residue called 1,3-propanediol in a predetermined position within the PCR primer, which can yield compatible 5′-ends for cloning, however, this method is much less efficient than other ligase-independent cloning methods (Kaluz and Flint 1994).

iv) PCR-Directed Cloning

PCR-specific cloning methods are often one-step procedures in which the recombinant DNA is produced during the amplification procedure itself. There are many variations on this theme, in which some are ligase-dependent and others are not. These methods are primarily used to produce site-specific mutations in cloned genes. A brief description of the current techniques follows.

Ligase-Dependent Methods

a) Stratagene have commercialized a technique for the cloning of blunt-end PCR fragments (Weiner 1993), originally described by Liu and Schwartz (1992). Their methodology requires phosphorylating the 5′ end of the PCR primers. The recipient vector is linearized and treated with calf intestinal alkaline phosphatase (CIAP) and then digested with a second restriction enzyme to yield compatible ends. This is a rather convoluted technique but the resultant vector is mono-phosphorylated and allows for directional cloning. They reported a 95% success rate for directional cloning, however their technique requires an ethanol precipitation and still relies on the actions of ligase.

b) “Hetero-stagger cloning” is another ligase-dependent method which requires a total of four PCR primers (Liu 1996). One set of primers is the traditional PCR primer pair and the second set is equivalent to the first, but includes three additional 5′-GGG residues. The DNA is amplified under normal PCR conditions, the products are denatured by heat and then allowed to reanneal slowly by cooling. Reannealing results in the formation of four distinct species. Only 50% of the products are theoretically cloneable, and only 25% of the products would successfully result in directional clones. The only claimed advantage to this technique is that it allows for modern proofreading polymerases to be used during amplification.

c) A variation of the staggered re-annealing technique has also been used which requires only one primer pair (Ailenberg and Silverman 1996).

d) More recently, Gal et al., (1999) have devised a technique called “autosticky PCR” (AS-PCR) (patent application HU9801320). This technique takes advantage of the observation that abasic sites present in DNA can stall DNA polymerases. In this method, PCR primers are designed to contain abasic sites, which stall the amplifying polymerase, resulting in 5′-overhangs thus enabling ligation into a suitably digested vector. The abasic site is produced by the incorporation of tetrahydrofuran, a stable structural analogue of 2-deoxyribose, at the desired position. This method does provide for directional-cloning, but requires non-traditional reagents and an overnight ligation is recommended.

Ligase-Independent Cloning Methods (LIC)

a) The original ligase PCR-cloning method was described by Shuldiner et al., (1991). Since then, numerous adaptations of this technique have been developed. The technique described here (Temesgen and Eschrich 1996) requires three PCR primers, in which one of the primers contains an additional 24 nucleotides. This process involves two distinct PCR amplifications, thus increasing the probability of introducing PCR errors into the products. However, the linear products can be directly transformed into E. coli obviating the need for ligase. Competent E. coli strain TG2 cells are required, and it is unclear if classical strains such as JM105 or DH-5α are able to be substituted. This technique does provide for directional cloning, although the success is related to the PCR parameters in the second PCR step. Any vector can be used in the technique and no restriction enzymes are needed.

b) Garces and Laborda (1995) reported a similar technique only requiring two PCR primers, one of which has a 20 bp 5′-extension. The reaction occurs within a single-tube reaction, and can be adapted for use with any vector, but the efficiency is greatly affected by the PCR parameters.

v) In Vivo Recombination-Based Cloning

PCR-cloning is traditionally completed within the test-tube environment of the laboratory, however, there are at least two reports of cloning using in vivo systems. The following technique was based on the observation that when yeast were co-transfected with a linear template and a gapped plasmid, homologous recombination was able to “patch” the two species together (Guthrie and Fink, 1991). PCR products have since been cloned in yeast using this method (Scharer and Iggo 1992). A similar phenomenon has been reported in E. coli (Oliner, Kinzler et al. 1993). This technique presumably takes advantage of endogenous exonuclease or polymerase activities encoded by the host, but there is no speculation as to what is exactly occurring. The PCR primers are designed to contain 5′-sequences which are identical to sequences adjacent to a chosen RE site. The linearized vector and the PCR products are co-transfected into E. coli strain JC8679. This technique may not be suitable for use with traditional E. coli strains because independent reports indicate that DH5α cells cannot catalyze intramolecular gap repair, and thus might not be expected to catalyze inter-molecular recombination (Hanahan, 1985). A similar methodology described by Bubeck et al., (1993) reported successful recombination in DH5α cells but only if they were transformed by CaCl₂ methods. Two more commonly used techniques for bacterial transformation known as heat shock and electroporation were unsuccessfully used in the above experiment.

vi) Exonuclease-Based PCR Cloning

A completely different approach to the cloning of PCR fragments involves the generation of single-strand overhangs through the action of various exonucleases. All of the exo-based methods are ligase-independent and are based on the technique originally reported by Aslanidis and deJong, (1990). Numerous modifications to this technique have allowed for improvements in the method (Haun, Serventi et al. 1992; Kuijper, Wiren et al. 1992), both of which use the 3′-5′ exonuclease activity of T4 DNA polymerase. PCR primers are designed to contain a 5′-extension complementary to sequences adjacent to a chosen RE site within the vector. Single-strand overhangs are generated through the exonucleolytic digestion by T4 poi and annealing of single-strand regions between the vector and insert is sufficiently stable to allow for direct bacterial transformation. These techniques require delicate control of incubation periods, as these enzymes are extremely efficient, and if one is not careful, excess DNA can be digested. Kuijper et al., (1992) also reported that there is great variation between enzyme preparations, therefore, requiring fine-tuning of temporal conditions with each new batch of enzyme. A second drawback to these specific methods is the requirement for the addition of dTTPs or dATPs in the exo reaction to stop the enzyme at the appropriate positions.

A similar method to that reported above uses a different enzyme called exonuclease III (Hsiao 1993), which was originally used for cloning in 1992 (Kaluz, Kolble et al. 1992). Its limitation is that only blunt-ended or 5′-overhanging substrates can be efficiently cloned. Substrates with 3′-overhangs cannot be cloned by this method.

More recently, phage T7 Gene6 exonuclease has been used for PCR-cloning (Zhou and Hatahet 1995). In this technique PCR primers are designed to include internal phosphorothioate bonds positioned towards the center of the primers. The Tend of the primers are standard PCR primers, whereas the 5′ ends are designed to be complementary to sequences adjacent to a certain RE site. This method produces directional clones and is ligase-independent but requires the use of non-standard PCR primers. U.S. Pat. No. 5,580,759 (Yang, et al.) also discloses a method of construction of recombinant DNA by exonuclease recession.

In summary, a wide variety of methods exist for the cloning of PCR products, and each has its advantages and disadvantages. There remains a need for an optimal cloning method having the following characteristics:

compatible with the use of any vector and any restriction enzyme;

requires only two PCR primers comprised solely of natural bases;

ligase independent;

time efficient;

provides almost exclusively directional cloning;

only the terminal sequences of the amplified region need to be known;

no possibility of internal digestion of the PCR product;

any type of amplifying polymerase can be used;

compatible with various readily available E. coli strains;

transformation of bacteria can be accomplished through a variety of techniques;

unambiguous selection; and

adaptable to other techniques such as combinatorial cloning.

SUMMARY OF THE INVENTION

The present inventors have determined that DNA polymerase, such as vaccinia DNA polymerase, is able to efficiently join one or more linear DNA molecules. The method uses recombination between sequence elements present at the end(s) of a series of DNA molecules to specify the junctions and uses specific DNA polymerases to join the molecules. The method may be used to join one or more linear DNA molecules precisely in a single procedure. The primary application of this new method is in the construction of recombinant DNA molecules, as specifically applied to the cloning of PCR products into any desired vector. The present method offers all of the characteristics of an optimal cloning method listed above.

Accordingly, the present invention provides a method of joining two linear DNA molecules comprising the step of:

-   -   providing a first linear DNA molecule having a first end and a         second end;     -   providing a second linear DNA molecule having a first end and a         second end;     -   wherein the first linear DNA molecule has a sequence of         nucleotides at either the first end or the second end that is         complementary to a sequence of nucleotides at either the first         end or the second end of the second linear DNA molecule and     -   incubating the two linear DNA molecules in the presence of a DNA         polymerase under conditions whereby the two linear DNA molecules         are joined.

In one embodiment, the present invention provides a method of joining two or more linear DNA molecules comprising the steps of:

-   -   providing two or more linear DNA molecules, each having an x and         x′ strand, having opposite polarities, wherein the 5′ end of the         x′ strand of one linear DNA molecule has a sequence of         nucleotides that is complementary to the 5T end of the x strand         of another linear DNA molecule to which it is to be joined; and

incubating the two or more linear DNA molecules in the presence of a DNA polymerase under conditions whereby the two or more linear DNA molecules are joined;

wherein the DNA polymerase has intrinsic exonuclease activity and is capable of performing the DNA joining reaction of the invention.

This method may be used to join any number of DNA molecules. The key is to ensure that the molecules are selected such that the ends of each DNA molecule have complementary regions to the molecule it is to be joined to. Internal molecules must have complementary regions on both ends. Particular applications of this technology are the combinatorial fusion of DNA cassettes and preparation of synthetic genes. The technique is also useful for reconstruction of fragmented clones.

The method of the invention may also be applied to the recircularization of single DNA molecules in which the ends bear substantially complementary nucleic acid sequences. Application of this technique may be in the area of site-directed mutagenesis.

The DNA polymerases that may be used in the method of the invention include all DNA polymerases having intrinsic exonuclease activity, preferably 3′-5′ exonuclease activity, that are capable of performing the DNA joining reaction of the invention. Such a polymerase may be identified by assaying for its ability to join two linear DNA molecules, having ends with complementary nucleotide sequences, as described herein. Preferably the DNA polymerase is selected from the group consisting of vaccinia virus DNA polymerase, T4 DNA polymerase and the Klenow fragment of E. coli DNA polymerase I. Most preferably, the DNA polymerase is vaccinia virus DNA polymerase. The length of the complementary nucleotide sequence on each linear DNA molecule may be between about 5 and about 100 nucleotides, preferably between about 8 and about 50 nucleotides and, most preferably, between about 10 and 35 nucleotides. Various, well known stimulatory factors may be added to the incubation mixture. Such stimulatory factors are those that increase the efficiency of the reaction and stabilize the desired reaction products, for example, single strand DNA binding proteins.

In another of its embodiments, the present invention involves a method of constructing a recombinant. DNA molecule comprising the steps of:

-   -   providing a linearized vector DNA molecule and a template DNA         molecule, each having a first and a second end;     -   providing a first primer DNA molecule having a 5′ end that         comprises nucleotide sequences that will incorporate nucleotide         sequences that are complementary to the first end of the         linearized vector molecule onto the first end of the template         DNA molecule and a 3′ end that is designed to hybridize to a         suitable location on the first end of the template DNA molecule;     -   providing a second primer DNA molecule having a 5′ end that         comprises nucleotide sequences that will incorporate nucleotide         sequences that are complementary to the second end of the         linearized vector molecule onto the second end of the template         DNA molecule and a 3′ end that is designed to hybridize to a         suitable location on the second end of the template DNA         molecule;     -   amplifying the template DNA molecule using the polymerase chain         reaction with the first and second primers to generate a PCR         amplified product; and     -   incubating the PCR amplified product with the linearized vector         DNA molecule in the presence of a DNA polymerase to generate a         recombinant DNA molecule;

wherein the DNA polymerase has intrinsic exonuclease activity and is capable of performing the DNA joining reaction of the invention.

The DNA polymerases that may be used in the method of the invention include all DNA polymerases having intrinsic exonuclease activity, preferably exonuclease activity, that are capable of performing the DNA joining reaction of the invention. Such polymerases may be identified by assaying for the ability to join two linear DNA molecules having ends with complementary nucleotide sequences, as described herein. Preferably the DNA polymerase is selected from the group consisting of vaccinia virus DNA polymerase, T4 DNA polymerase and the Klenow fragment of E. coli DNA polymerase I. Most preferably, the DNA polymerase is vaccinia virus DNA polymerase. Various, Well known stimulatory factors may be added to the incubation mixture. Such stimulatory factors are those that increase the efficiency of the reaction and stabilize the desired reaction products, for example, single strand DNA binding proteins.

The number of complementary nucleotides that are incorporated onto the first and second ends of the template DNA molecule may be between about 5 and about 100 nucleotides, preferably between about 8 and about 50 nucleotides and, most preferably, between about 10 and 35 nucleotides.

This method could be readily applied to the insertion of two or more DNA molecules into a vector. Each additional molecule would require two further bipartite PCR primers, each having a first portion that primes a PCR extension that is complementary to the appropriate end of the adjacent molecule and a second portion that is complementary to the appropriate end of the DNA molecule to be amplified.

The linear DNA molecule to be inserted into a linearized vector using the method of the invention need not be obtained through PCR amplification. Therefore the present invention further involves a method of constructing a recombinant DNA molecule comprising:

-   -   providing a linearized vector DNA molecule;     -   providing a linear insert DNA molecule having ends that are         substantially complementary to the ends of the linearized vector         DNA molecule to which they are to be joined; and     -   incubating the linearized vector DNA molecule and linear insert         DNA molecule in the presence of a DNA polymerase under         conditions where the two DNA molecules are joined;

wherein the DNA polymerase has intrinsic exonuclease activity and joins the DNA molecules. The linear insert DNA molecule may be obtained by any known means, for example, chemical synthesis, ligation or annealing.

The present invention provides a method to directionally clone any template DNA molecule into a single restriction site of any vector. The vector ends may be generated from any restriction enzyme cleavage. The method does not require a ligation step nor the use of carefully controlled conditions as is required with methods involving specific exonucleases alone.

The present invention is also directed to kits containing reagents for conducting the method.

These and other aspects of the present invention will be described in greater detail hereinbelow.

BRIEF DESCRIPTION OF THE DRAWINGS

The features of the present invention will become more apparent from the following description in which reference is made to the appended drawings in which:

FIG. 1 shows a schematic representation (Panel A) and the experimental results (Panels B and C) for the joining of two linear DNA molecules using the method of the invention.

FIG. 2 shows a schematic representation (Panel A) and the experimental results (Panel B) for the joining of three linear DNA molecules using the method of the invention.

FIG. 3 shows a schematic representation of the application of the method of the invention to the combinatorial fusion of DNA cassettes.

FIG. 4 is a schematic showing the application of the method of the invention to the cloning of PCR products.

FIG. 5 shows a schematic representation and the experimental results for assays investigating the effect of overlapping and non-overlapping end homology in the DNA joining method of the invention.

FIG. 6 is a graph and experimental results (inset) showing the effect of vaccinia single strand binding protein on joint molecule formation using the method of the invention.

FIG. 7 provides a schematic representation and experimental results depicting the joining of three linear DNA substrates and the fate of 5′- and 3′-end labels during the joining of three linear DNA molecules using the method of the invention.

FIG. 8 provides schematic and experimental results for the cloning of PCR-amplified DNA using the method of the invention.

FIG. 9 shows a graphical representation of the effect of homology length on joint molecule formation in the method of the invention.

FIG. 10 provides a map of DNA to be recombined to clone a recombinant DNA pRP406-SFV using the method of the invention.

FIG. 11 shows the results of in vitro recombination of the linear DNA shown in FIG. 10 (0.8% agarose gel).

DETAILED DESCRIPTION OF THE INVENTION Definitions

The term in “complementary” as used herein, refers to nucleotide sequences in a single stranded molecule of DNA that are sufficiently complementary to a strand of nucleotide sequences in another DNA molecule to specifically (non-randomly) hybridize to it with consequent hydrogen bonding.

The term “linear DNA molecule” as used herein refers to a double stranded (duplex) nucleic acid molecule comprising two strands of opposite polarity (sense and antisense) of substantially complementary polynucleotides held together by one or more hydrogen bonds between each of the complementary bases present in a base pair of the molecule.

The term “recombinant DNA molecule” as used herein refers to a hybrid DNA molecule comprising at least two nucleotide sequences not normally found together in nature.

The term “nucleotide” as used herein refers to a monomeric unit of DNA consisting of a sugar moiety (pentose), a phosphate group and a nitrogenous heterocyclic base. The base is linked to the sugar moiety via the glycosidic carbon (I′ carbon of pentose) and that combination of base and sugar is a nucleoside. When the nucleoside contains a phosphate group bonded to the 3′ or 5′ position of the pentose it is referred to as a nucleotide. A sequence of operatively linked nucleotides is typically referred to herein as a “nucleotide sequence”, and their grammatical equivalents, and is represented by a formula whose left to right orientation is in the conventional direction of 5′-terminus to 3′-terminus.

DNA Joining Methods

The present invention relates to a method to join two or more linear DNA molecules using specific DNA polymerases. The method relies on the ability of specific DNA polymerases to facilitate the recombination of linear DNA molecules having ends that share complementary nucleotides.

Accordingly, the present invention provides a method of joining two linear DNA molecules comprising the step of:

-   -   providing a first linear DNA molecule having a first end and a         second end;     -   providing a second linear DNA molecule having a first end and a         second end,     -   wherein the first DNA molecule has a sequence of nucleotides at         either the first end or the second end that is complementary to         a sequence of nucleotides at either the first end or the second         end of the second linear DNA molecule; and     -   incubating the two linear DNA molecules in the presence of a DNA         polymerase under conditions whereby the two linear DNA molecules         are joined.

The first and/or second linear DNA molecule can be comprised of one or more linear DNA molecules. For example, the first linear DNA molecule may consist of two linear DNA molecules that have been previously joined using the method of the invention.

In one embodiment, the present invention provides a method of joining two or more linear DNA molecules comprising the steps of:

-   -   providing two or more linear DNA molecules, each having an x and         x′ strand having opposite polarities, wherein the 5′ end of the         x′ strand of each linear DNA molecule has a sequence of         nucleotides that is complementary to a sequence of nucleotides         at the 5′ end of the x strand of the linear DNA molecule to         which it is to be joined; and     -   incubating the two or more linear DNA molecules in the presence         of a DNA polymerase under conditions whereby the two or more         linear DNA molecules are joined;

wherein the DNA polymerase has intrinsic exonuclease activity and is capable of performing the DNA joining reaction of the invention.

DNA polymerases that work in the methods of the invention are those having intrinsic exonuclease activity, preferably 3′-5′ exonuclease activity, that are capable of performing the DNA joining reaction of the invention. Such polymerases may be identified by assaying for the ability to join two linear DNA molecules having ends with complementary nucleotide sequences as described in Experiment 2 herein (Experimental Section). Purified vaccinia DNA polymerase was used in the examples presented herein. The reaction has also been shown to work with T4 DNA polymerase and the Klenow fragment of E. coli DNA polymerase I. The DNA polymerases of the invention are either commercially available or may be prepared using standard recombinant DNA technology. For example, vaccinia DNA polymerase may be purified from vaccinia-infected BSC-40 cells as described in McDonald and Traktman (1994) and Willer, Mann et al. (1999). Alternatively, vaccinia DNA polymerase may be purified from cells infected with wild-type vaccinia virus. We assay polymerases to measure their ability to join two linear DNA molecules having ends with complementary nucleotide sequences. These include but are not limited to, those encoded by bacteriophage (e.g. T4, T7), bacteria (e.g. E. coli), fungi (e.g. S. cerevisiae) and viruses (e.g. poxviruses, herpes viruses, adenoviruses, African swine fever virus and other Iridoviruses, and Bacculoviruses). The DNA polymerases useful in the invention preferably have intrinsic 3′-5′ exonuclease activity. The invention also extends to cover those DNA polymerases with 5′-3′ exonuclease activity.

Various known stimulatory factors may be added to the incubation mixture to enhance the efficiency of the reaction and/or stabilize the reaction products. Suitable stimulatory factors include single strand DNA binding proteins. Some single strand DNA binding proteins that may be used include, but are not limited to, vaccinia and E. coli single strand binding proteins, Herpes simplex virus ICP8 protein, and yeast and human replication Protein A (eg. yRPA and hRPA). A skilled person would be able to readily identify other suitable stimulatory factors that may be usefully combined with a DNA polymerase in the methods of the invention. In one aspect of the invention, the vaccinia single strand binding protein is used to enhance the yield of a DNA joining reaction employing vaccinia DNA polymerase.

The degree of complementation between the ends of the linear DNA molecules can vary from between about 5 and about 100 nucleotides, preferably between about 8 and about 50 nucleotides and, most preferably, between about 10 and 35 nucleotides. The linear DNA molecules that may be joined using the method of the invention may be obtained from genomic DNA of prokaryotic or eukaryotic genomes, as well as from various vectors, including plasmids, cosmids, phage, BACs and the like, using restriction enzyme cleavage. Alternatively, the linear DNA molecule may be synthesized by chemical techniques, for example, using automated synthesis and the like. The DNA molecule may also be derived from RNA species, such as mRNA, tRNA and rRNA, from any species and may first be converted to cDNA by reverse transcriptase and the amplified as described in Sambrook et al. (1989).

In its most general application, the present invention provides a method to join two or more linear DNA molecules. FIG. 1 shows a schematic of this reaction for the joining of two linear DNA molecules (Panel A). This illustrates how two substrates sharing complementary sequences on the left and right ends can be incubated in the presence of a specific DNA polymerase to form a dimer. Panel C of FIG. 1 shows the results from an experiment where a 1:1 mixture of two substrates, sharing 35 bp of complementary sequence at the left and right ends, was incubated with varying quantities of vaccinia DNA polymerase and the products separated by size using an agarose gel. No reaction is observed when the polymerase is omitted (lane 2) and increasing yields of products were seen when increasing amounts of polymerase were added (lanes 3-9).

FIG. 2, Panel A, shows the joining of three linear DNA molecules to produce a trimer. In this case the “middle” molecule must have sequences of DNA on each end that are complementary to the ends of the two flanking molecules. The results from an actual experiment where the middle molecule had about 20 bp of complementary DNA sequences with the two flanking molecules on each end are shown in Panel B of FIG. 2. The results in Panel B of FIG. 2, also illustrate an important control (lane 5). The polymerase will not form concatemers when provided with just one of the three substrates, since the ends of identical molecules do not share the appropriate type of complementation. This specificity means that one can direct exactly how two or more molecules are fused, simply by controlling a nearly infinite array of terminal sequence overlaps.

Accordingly, the present invention provides a method of joining three linear DNA molecules comprising:

-   -   providing a first DNA molecule having a first end and a second         end;     -   providing a second linear DNA molecule having a first end and a         second end;     -   providing a third linear DNA molecule having a first end and a         second end;     -   wherein the first linear DNA molecule has a sequence of         nucleotides at the first end that is complementary to a sequence         of nucleotides at either the first or the second end of the         second linear DNA molecule and wherein the first linear DNA         molecule has a sequence of nucleotides at the second end that is         complementary to a sequence of nucleotides at either the first         or the second end of the third linear DNA molecule, and     -   incubating the three linear DNA molecules in the presence of a         DNA polymerase under conditions whereby the three linear DNA         molecules are joined.

One skilled in the art will appreciate that the above method can be used to join any number of DNA molecules provided the DNA molecules contain the appropriate complementary sequences to join one molecule to another. For example, to join a fourth DNA molecule to the three DNA molecules described above, either the second or third DNA molecule will have a sequence of nucleotides at its free end (i.e. the end that is not joined to the first DNA molecule) that is complementary to a sequence on one end of the fourth DNA molecule.

Another application of the present invention is in the combinatorial fusion of DNA cassettes as illustrated in FIG. 3. In this example, three different pools of DNA molecules are prepared. Within a pool of molecules, the central portion of each molecule varies in sequence while the ends are identical. For example, as shown in FIG. 3, A1-A5 all have the same about 5 to about 100, preferably about 8 to about 50, more preferably about 10 to about 35, nucleotide sequences at the right end, but the remaining portion of the molecules vary in sequence. The left ends of the molecules in the “B” pool are compatible with the right ends of molecules in the “A” pool. Similarly, the left ends of the molecules in the “C” pool are compatible with the right ends of molecules in the “B” pool. By compatible, it is meant that they share appropriate complementary sequences ranging from about 5 to about 100; preferably about 8 to about 50, more preferably about 10 to about 35, nucleotides. Incubation of the mixture of molecules from pools A, B and C with a DNA polymerase useful in the method of the invention will create trimers composed of one of each of the molecules selected from the A, B, and C pools. The resulting pool of trimers should express a random assortment of “A”, “B” and “C” variants. The number of “pools” and molecules within each pool could be varied to potentially produce a random assortment of millions of different DNA molecules. The combinatorial fusion of DNA cassettes using the method of the invention may be applied to the construction of DNA sequences encoding novel proteins through the combinatorial fusion of DNA molecules encoding different protein structural domains. These libraries of proteins may be screened for novel binding specificities.

The method of the invention may also be used to recombine (circularize) a single DNA molecule in which the ends bear substantially complementary nucleic acid sequences. Therefore, the present invention also relates to a method of circularizing linear DNA molecules comprising:

-   -   PCR amplifying a linear DNA molecule in the presence of primers         that will introduce substantially complementary nucleic acid         sequences onto each end of the linear DNA molecule; and     -   incubating the PCR amplified linear DNA molecule in the presence         of a DNA polymerase under conditions where the linear DNA         molecule is circularized:

wherein the DNA polymerase has intrinsic exonuclease activity and circularizes the DNA molecule.

One use for the application of the method of the invention to the circularization of single DNA molecules is in the area of site directed mutagenesis. For example, a plasmid comprising a gene of interest could be PCR amplified using primers designed to incorporate substantially complementary nucleic acid sequences on each end. If one designed the primers so that mutations are introduced into the plasmid within the gene of interest, mutated forms of the gene may be obtained.

Several additional reaction features were investigated. Perhaps most important is the fact that vaccinia polymerase does not seem to care what type of ends are present on the two recombining molecules. Molecules bearing 5′ overhanging, 3′ overhanging or blunt ends, in any pairwise combination, were still substrates as long as the two molecules shared appropriate sequence complementation.

DNA Cloning Methods

In another of its embodiments, the present invention provides a method of cloning any double stranded PCR product into any vector. Therefore there is provided, a method of constructing a recombinant DNA molecule comprising the steps of:

-   -   providing a linearized vector DNA molecule and a template DNA         molecule, each having a first and a second end;     -   providing a first primer DNA molecule having a 5′ end that         comprises nucleotide sequences that will incorporate nucleotide         sequences that are complementary to the first end of the         linearized vector molecule onto the first end of the template         DNA molecule and a 3′ end that is designed to hybridize to a         suitable location on the first end of the template DNA molecule;     -   providing a second primer DNA molecule having a 5′ end that         comprises nucleotide sequences that will incorporate nucleotide         sequences that are complementary to the second end of the         linearized vector molecule onto the second end of the template         DNA molecule and a 3′ end that is designed to hybridize to a         suitable location on the second end of the template DNA         molecule;     -   amplifying the template DNA molecule using the polymerase chain         reaction with the first and second primers to provide a PCR         amplified product; and incubating the PCR amplified product with         the linearized vector DNA molecule in the presence of a DNA         polymerase to generate a recombinant DNA molecule;

wherein the DNA polymerase has intrinsic exonuclease activity and is capable of performing the DNA joining reaction of the invention.

In this method, all that is required is that the PCR primers be extended to incorporate some nucleotides that duplicate the base sequence flanking the chosen cloning site in the vector. The suggested approach is illustrated in FIG. 4. A set of two bipartite primers is designed. The 3′ end of the first primer molecule is designed to hybridize with the first end of the template DNA molecule, and the 5′ end of the first primer molecule has a sequence of from about 5 to about 100, preferably about 8 to about 50, more preferably about 10 to about 35, nucleotides that are designed to incorporate sequences in the final PCR product that are complementary to the first end of the vector DNA molecule. The 3′ end of the second primer is designed to hybridize with the second end of the template DNA molecule, and the 5′ end of the second primer molecule has a sequence of from about 5 to about 100, preferably about 8 to about 50, more preferably about 10 to about 35, nucleotides that are designed to incorporate sequences in the final PCR product that are complementary to the second end of the vector DNA molecule. The two primers are then annealed to the template DNA molecule which is then PCR amplified using standard conditions to generate a PCR amplified product. The vector is prepared by treating it with the appropriate restriction enzyme to cut it at the chosen insert site using standard conditions.

The term primer as used herein is meant to describe a bipartite primer or a primer having a first and second portion. A first portion of the primer is designed to be complementary to the appropriate end of a template DNA molecule and a second portion of the primer is designed to be complementary to nucleotide sequences on one side of the chosen restriction site of the vector. The bipartite oligonucleotide primers of the present invention may be broadly defined as single stranded oligonucleotides that are complementary to DNA molecules of interest and will allow the DNA molecules to be incorporated into a vector. Bipartite primers will generally have a minimum length of about 18 nucleotides and a maximum length of about 200 nucleotides, preferably about from 25 nucleotides to about 100 nucleotides, more preferably from about 30 nucleotides and about 40 nucleotides. This method could be readily applied to the insertion of two or more DNA molecules into a vector. Each additional molecule would require two further bipartite PCR primers, each having a first portion that primes a PCR extension that is complementary to the appropriate end of the adjacent molecule and a second portion that is complementary to the appropriate end of the DNA molecule to be amplified.

The PCR amplified product and the linearized vector are then incubated in a suitable reaction buffer in the presence of a DNA polymerase having intrinsic exonuclease activity, preferably 3′-5′ exonuclease activity, that is capable of performing the DNA joining reaction of the invention, for about 5 to about 60 minutes, preferably from about 10 to about 40 minutes, most preferably from about 15 to about 30 minutes. Purified vaccinia DNA polymerase was used in the examples presented herein. The reaction has also been shown to work with T4 DNA polymerase and the Klenow fragment of E. coli DNA polymerase I. The reaction buffer may be any buffer that is used in DNA annealing reactions. The temperature may be in the range of from about 35-40° C., more preferably about 37° C.

The DNA polymerases that work in this method may be identified by assaying for the ability to join two linear DNA molecules having ends with appropriate complementary sequences as describe in Example 2 herein (Experimental Section). The DNA polymerases of the invention are either commercially available or may be prepared using standard recombinant DNA technology. For example, vaccinia DNA polymerase may be purified from vaccinia-infected BSC-40 cells as described in McDonald and Traktman (1994) and Willer, Mann et al. (1999). Alternatively, vaccinia DNA polymerase may be purified from cells infected with wild-type vaccinia virus. We assay polymerases to measure their ability to join two linear DNA molecules having ends with complementary nucleotide sequences. These include, but are not limited to, those encoded by bacteriophage (e.g. T4, T7), bacteria (e.g. E. coli), fungi (e.g. S. cerevisiae) and viruses (e.g. poxviruses, herpes viruses, adenoviruses, African swine fever virus and other Iridoviruses, and Bacculoviruses). The DNA polymerases useful in the invention preferably have intrinsic 3′-5′ exonulcease activity. The invention also extends to cover those DNA polymerases with 5′-3′ exonulcease activity.

Various known stimulatory factors may be added to the incubation mixture to enhance the efficiency of the reaction and/or stabilize the reaction products. Suitable stimulatory factors include single strand DNA binding proteins. Some single strand DNA binding proteins that may be used include, but are not limited to, vaccinia and E. coli single strand binding proteins, Herpes simplex virus ICP8 protein, and yeast and human replication Protein A (eg. yRPA and hRPA). A skilled person would be able to readily identify other suitable stimulatory factors that may be usefully combined with a DNA polymerase in the methods of the invention. In one aspect of the invention, the vaccinia single strand binding protein is used to enhance the yield of a DNA cloning method of the invention employing vaccinia DNA polymerase.

The method of the invention may be used to PCR clone any variety or number of target DNA molecules. The only limitation on size is the capacity of the vector molecule to carry the insert in transformation and replication in the host cell. Any vector capable of replicating in a prokaryotic or eukaryotic cell is usable with the present invention, such as plasmids, cosmids, phage, BACs and the like. The choice of vector depends on the functional properties desired, for example, protein expression, and the host cell to be transformed. Preferably, the vector has a known sequence of about 5 to about 100, preferably about 8 to about 50, most preferably about 10 to about 35 nucleotides, on either side of the chosen restriction enzyme site. The DNA molecules that may be incorporated into a recombinant DNA molecule using the method of the invention may be obtained from genomic DNA of prokaryotic or eukaryotic genomes, as well as from various vectors, including plasmids, cosmids, phage, BACs and the like, using restriction enzyme cleavage. Alternatively, the DNA molecules may also be synthesized by automated synthesis and the like. The nucleic acid may also be derived from RNA species, such as mRNA, tRNA and rRNA, from any species and may first be converted to cDNA by reverse transcriptase and the amplified as described in Sambrook et al. (1989).

The linear DNA molecule to be inserted into a linearized vector using the method of the invention need not be obtained through PCR amplification. Such a molecule may also be prepared by linearization of a circular double strand DNA molecule by restriction enzyme digestion, with subsequent attachment of synthetic oligomer linkers onto the ends, or secondary digestion of an already linear DNA molecule with restriction enzymes, followed by addition of adapter/linkers onto the ends, or by annealing of two appropriately designed synthetic single strand DNA oligomers which can be annealed to form an intact duplex DNA molecule, or any other related method. Incubation of a linear DNA molecule, obtained by such a method, with a linearized vector DNA molecule in the presence of a DNA polymerase, having intrinsic exonuclease activity, will provide the desired recombinant DNA molecule. Therefore the present invention also relates to a method of constructing a recombinant DNA molecule comprising:

-   -   providing a linearized vector DNA molecule;     -   providing a linear insert DNA molecule having ends that are         substantially complementary to the ends of the linearized vector         DNA molecule to which they are to be joined; and     -   incubating the linearized vector DNA molecule and linear insert         DNA molecule in the presence of a DNA polymerase under         conditions where the two DNA molecules are joined;

wherein the DNA polymerase has intrinsic exonuclease activity and joins the DNA molecules.

Transformation of Recombinant DNA Molecules

The reaction mixture obtained from the incubation of DNA polymerase with the linearized vector and the PCR amplified product may be used directly to transform any host cell using standard transformation procedures. Therefore the present invention also provides a method to produce a recombinant DNA product comprising the steps of:

-   -   providing a linearized vector DNA molecule and a template DNA         molecule, each having a first and a second end;     -   providing a first primer DNA molecule having a 5′ end that         comprises nucleotide sequences that will incorporate nucleotide         sequences that are complementary to the first end of the         linearized vector molecule onto the first end of the template         DNA molecule and a 3′ end that is designed to hybridize to a         suitable location on the first end of the template DNA molecule;     -   providing a second primer DNA molecule having a 5′ end that         comprises nucleotide sequences that will incorporate nucleotide         sequences that are complementary to the second end of the         linearized vector molecule onto the second end of the template         DNA molecule and a 3′ end that is designed to hybridize to a         suitable location on the second end of the template DNA         molecule;     -   providing the template DNA molecule using the polymerase chain         reaction with the first and second primers to provide a PCR         amplified product;     -   incubating the PCR amplified product with the linearized vector         DNA molecule in the presence of a DNA polymerase to generate a         recombinant DNA molecule;     -   transforming the recombinant DNA molecule into a host cell; and     -   isolating the recombinant DNA product;

wherein the DNA polymerase has intrinsic exonuclease activity and is capable of performing the DNA joining reaction of the invention. A suitable stimulatory factor may optionally be used in the methods of the invention. For example, one may incubate the PCR amplified product with the linearized vector DNA molecule in the presence of a DNA polymerase and a single strand DNA binding protein to generate a recombinant DNA molecule.

Any variety of cell that is transformable may serve as a host cell, such as E. coli SURE, JM105. DH5α, HB101, XL1-blue and the like. Other bacterial hosts may include Bacillus or Pseudomonas species and the like. By way of example, eukaryotic host cells may include Saccharomyces species. One of the advantages of the present invention is that the method is selective for the correct orientation of the insert DNA. Therefore, host cells that have been transformed by a recombinant vector will have the insert DNA in the correct orientation in that vector.

The invention extends to cover the transformation of host cells with reaction products obtained from the cloning of any linear DNA molecule into a linearized vector molecule using the method of the invention. The linear DNA molecule to be cloned may be prepared using PCR as described above or by linearization of a circular dsDNA molecule by restriction enzyme digestion, with subsequent attachment of synthetic oligomer linkers onto the ends, or secondary digestion of an already linear DNA molecule with restriction enzymes, followed by addition of adapter/linkers onto the ends, or by annealing of two appropriately designed synthetic ssDNA oligomers which can be annealed to form an intact duplex DNA molecule, or any other related method.

Kits

The present invention also provides kits suitable for directionally cloning PCR products (or any other linear DNA molecule with appropriate homologous nucleotides on the ends) into a linearized vector. The kit may comprise, in separate containers, an aliquot of a DNA polymerase having intrinsic exonuclease activity that is capable of performing the DNA joining reaction of the invention and an aliquot of reaction buffer. An aliquot refers to an amount of the component sufficient to perform at least one program of cloning. The DNA polymerase may be provided as a solution of known concentration, in a buffer optionally comprising a suitable stabilizer, or may be provided as a predetermined aliquot of a freeze-dried product for dissolution in a suitable buffer. Optionally, the kit may comprise an aliquot of a stimulatory factor such as a single strand DNA binding protein. The kit may also comprise reagents required to perform a positive control reaction. Such reagents may include, in separate containers, an aliquot of linearized vector, an aliquot of insert DNA with first and second ends having appropriate complementary sequences, an aliquot of DNA polymerase having intrinsic exonuclease activity that is capable of performing the DNA joining reaction of the invention, optionally, an aliquot of a stimulatory factor such as a single strand DNA binding protein, and an aliquot of reaction buffer.

The present invention will be further illustrated in the following examples. However, it is to be understood that these examples are for illustrative purposes only, and should not be used to limit the scope of the present invention in any manner.

EXPERIMENTAL EXAMPLES Materials and Methods

Linear substrates were prepared by restriction enzyme digestion of plasmid pDW101, followed by phenol extraction and ethanol precipitation. pDW101 derives from pBluescript (KS+) (Stratagene) through a spontaneous deletion of nucleotides 618, 619 and 621. In some experiments, the linear substrates were purified by agarose electrophoresis and extracted from the agarose using a Geneclean II kit (New England Biolabs). [α-³²P] dCTP and [γ-³²P] dATP were purchased from NEN/Mandel Scientific. End labeled substrates were generated by treatment with shrimp alkaline phosphatase (United States Biochemical, Cleveland), followed by incubation with either T4 polynucleotide kinase and [γ-³²P] dATP (3000 Ci/mmol) or Klenow enzyme and [α-³²P] dCTP (3000 Ci/mmol). Unincorporated radionucleotides were removed by G-25 spin columns (Pharmacia) and radioactivity was quantitated by Cherenkov (Schneider, 1971). HindIII-digested lambda phage DNA and HaeIII-digested ΦX174 DNA markers were purchased from New England Biolabs. Luciferase assay kit was purchased from Promega.

Cell and Virus Culture

BSC-40 cells were kindly provided by Dr. E. Niles (SUNY, Buffalo) and grown at 37° C. in DMEM (Gibco BRL) supplemented with 1% nonessential amino acids and 5% fetal calf serum in a 5% CO₂ environment Vaccinia virus (strain WR) was purchased from the ATCC.

Experiment 1 Vaccinia DNA Polymerase Purification

Purification of vaccinia DNA polymerase from vaccinia-infected BSC-40 cells has been described (McDonald and Traktman 1994; Willer, Mann et al. 1999). Briefly, a crude lysate from 60 150-cm² dishes of BSC40 cells co-infected with vTMPOL and VTF7.5 was subjected to purification through DEAE cellulose, phosphocellulose, ceramic hydroxyapatite and HiTrap heparin columns. Active fractions eluting at each chromatographic step were determined by DNA polymerase assays (Willer, Mann et al. 1999). Protein purity was determined by silver staining of denaturing polyacrylamide gels. Protein concentrations were assayed by using a dye-binding assay (Biorad) and a bovine serum albumin standard.

Experiment 2 Assay for Correct DNA Polymerase Activity

We measure the intrinsic strand joining activity of DNA polymerases, such as those encoded by bacteriophage (e.g. T4, T7), bacteria (e.g. E. coli), fungi (e.g. S. cerevisiae) and viruses (e.g. poxviruses, herpes viruses, adenoviruses, African swine fever virus and other Iridoviruses, and Bacculoviruses). The polymerases are assayed to measure their activity in the DNA joining reaction by incubating a reaction mixture comprising 30 mM Tris-HCl (pH 7.9), 5 mM MgCl₂, 70 mM NaCl, 1.8 mM dithiothreitol, 88 μg/mL acetylated BSA, 350 ng of each of a first and second linear DNA substrate and the polymerase to be assayed. The first and second linear DNA substrate must have complementary nucleotide sequences on their right and left ends respectively and may be obtained by a variety of methods including chemical synthesis and derivation of nucleic acid fragments from native nucleic acid sequences existing as genes, or parts of genes, in a genome, plasmid, or other vector, such as by restriction endonuclease digest (see, for e.g., preparation of linear substrates described in the Materials and Methods section above). The polymerase has the required activity if the formation of dimers is detected on an agarose gel stained with ethidium bromide. A preferred polymerase will allow the formation of more than about 1% of dimeric products.

Experiment 3 DNA Joining Reactions

Standard DNA joining reactions (20 μL) contained 30 mM Tris-1-HCl (pH 7.9), 5 mM MgCl₂, 70 mM NaCl, 1.8 mM dithiothreitol, 88 μg/mL acetylated BSA, 350 ng of each linear substrate, and varying quantities (usually 0.1 μg) of purified vaccinia DNA polymerase. DNA joining reactions employing single strand binding protein also included 25 μg/mL of recombinant vaccinia single strand binding protein (thought to be the IL3 gene product, Tseng et al. 1999) in the reaction mix. Reactions were incubated at 37° C. for 20 min, deproteinized and the reaction products were separated through a 0.8% agarose gel as described previously (Zhang and Evans, 1993). Ethidium-stained gels were photographed under UV illumination using Polaroid 665 film. DNA quantitation was determined by densitometry.

Joining of Two Linear Substrates:

To show that vaccinia DNA polymerase can catalyze strand joining reactions, two linear duplex substrates, sharing a small amount of overlapping sequence homology at the ends of the molecules, were prepared. This was accomplished by cutting pDW101 (SEQ. ID. NO. 1) with EcoRI (SEQ. ID. NO. 2) and XhoI (SEQ. ID. NO. 3) (FIG. 1A), leaving 33 bp of properly oriented sequences. DNA polymerase was then incubated with these DNAs and assayed for concatemer-forming activity using gel electrophoresis. It observed that the polymerase converted 45% of the input DNA into dimeric products over a 10 min period, with a concomitant loss of monomeric molecules (FIG. 1B). The yield of dimer declined slightly thereafter, stabilizing with about 35% of the molecules converted to product. The reaction yield was also dependent upon protein concentration (FIG. 1C).

Duplex Annealing Selectively Pairs Homologous Ends:

This pairing reaction required two different DNA substrates sharing some small amount of overlapping end homology. Controls showed that the reaction cannot produce joint molecules when the only available substrates were a pool of identical duplexes (FIG. 5, lanes 1-6). To determine which ends of the two substrates were being joined, EcoRI and XhoI cut molecules were further digested with ScaI, producing DNA fragments that can be differentiated by size (FIG. 5, inset). Vaccinia DNA polymerase selectively joined the two molecules sharing a segment of DNA bounded by the XhoI and EcoRI sites, as judged by the appearance of recombinants 4.2, 4.8, and 3.0 kbp in length (FIG. 5, lanes 9, 11, and 13, respectively). Such product sizes are consistent with these molecules being composed of the 3.0+1.2, 3.0+1.8, and 1.2+1.8 kbp DNA fragments encoding the XhoI-EcoRI interval.

The restriction enzymes used to prepare the interacting ends shown in FIGS. 1 and 5 leave 5′-overhanging ends with 4 nt overhangs. To test whether ends also affected reaction efficiency, various substrates were prepared by cutting pDW101 with different restriction enzymes. All possible combinations of molecules bearing 5′-overhanging, blunt, or 5′-recessed ends were then tested to see whether they were still substrates. It was found that vaccinia polymerase has no end preference. There was also no obvious correlation between the yield of duplex product and the length of sequence overlap, when the length of shared end homology ranged from 18 to 84 bp.

Other Reactions:

The effect of adding MgCl₂, spermidine, or vaccinia virus single strand binging protein (SSB) on the reaction efficiency was examined using KpnI- and NotI-cut substrates sharing 84 bp of overlapping homology. Magnesium had a reaction optimum of ˜10 mM. However, 20 mM MgCl₂ inhibited the reaction, as did spermidine concentrations exceeding 1 mM. The effects of adding recombinant vaccinia SSB (Tseng et al., 1999) were investigated. The principle replicative high-affinity single-strand DNA binding protein (SSB) is thought to be the I3L gene product (Rochester and Traktman, 1998; Tseng et al., 1999). Vaccinia SSB enhanced the yield of joint molecules 2-3-fold when added at concentrations between 25 and 100 μg/mL (FIG. 6). The net result was that over 80% of the substrate DNAs could be converted to dimers under these optimized reaction conditions.

Joining of Multiple Substrates:

The DNA-joining reaction can also recombine multiple substrates into higher-order concatemers and this can be exploited to provide further insights into the reaction mechanism. The plasmid pDW101 was cut with restriction enzymes so that the “middle” substrate (FIG. 7, molecule “B”) shared sequences in common with either end of two additional molecules (“A” and “C”). Alone, the middle duplex was not a substrate for the polymerase catalyzed reaction (FIG. 7, lanes 1 and 4). However, when the three substrates were incubated together with vaccinia polymerase in standard assays, they were rapidly converted into a mixture of dimers and trimers (FIG. 7, lanes 3 and 6). A small amount of the DNA (˜2%) was also converted into higher-order multimers whose structure is uncertain.

For the middle molecule to have been incorporated into a linear trimer, both ends of the molecule must have been subjected to enzymatic processing. To study any modifications which might have been introduced into the ends of these molecules, the HindIII-restricted (SEQ. ID. NO. 4) substrate was labeled and monitored the ³²P-label using autoradiography. The ³²P-labels were incorporated into the middle substrates using T4 polynucleotide kinase or Klenow polymerase, to see whether 3′ or 5′ end-labels suffered different fates. After electrophoresis and ethidium staining, the gel was fixed and autoradiographed to locate the label. It was clear, from inspection of the ethidium-stained gel, that duplex “B” was efficiently incorporated into concatemers regardless of whether it had been labeled on the 3′ or on the 5′ end (FIG. 7, lanes 3 and 6). However, whereas most of the 5′ label was incorporated into trimeric concatemers (FIG. 7, lane 3), none of the 3′-end label was retained in these molecules (FIG. 7, lane 6) or in the unreacted polymerase-treated substrate (FIG. 7, lane 4). These data, plus the MgCl₂ effect, suggests that the vaccinia polymerase 3′-5′ exonuclease plays a key role in joint molecule production in vitro. Although it is the 3′-5′ exonuclease activity of vaccinia DNA polymerase that plays a pivotal roll in the DNA joining reactions described herein, the reaction could work equally as well with DNA polymerases having 5′-3′ exonuclease activity.

If this reaction is dependent upon the activity of the 3′-5′ exonuclease of vaccinia DNA polymerase, one would predict that dNTPs should inhibit end-joining by inhibiting the nuclease. Experiments confirmed this prediction. Adding 1 μM (total) of all four dNTPs reduced the yield about 50%, while little if any joint molecules were formed in reactions containing >5 μM dNTPs. Dideoxyribonucleotides were also inhibitory, but only at much higher concentrations (>50 mM).

Example 4 PCR Step

A ˜800 bp region from a BamHI clone-derived from Shope Fibroma Virus (Wills, Delange et al. 1983; Delange, Macaulay et al. 1984) chosen at random was amplified using the PCR primers shown below. Capital letters represent the sequence complementary to the vector (pDW101) and small letters represent the sequence complementary to viral DNA sequence. PCR primers were designed to include complementary sequences from the vector adjacent to the recognition site for the restriction enzyme NotI.

Primer #1: (SEQ. ID. N0. 5) 5′ TTCTAGAGCGGCCagaaacaggcatcttacgcgtg 3′ Primer #2: (SEQ. ID. N0. 6) 5′ TCCACCGCGGTGGCGGCCacggaaacgccttggt 3′

Example 5 Vector Preparation

The vector pDW101 was digested with NotI as depicted below:

                             ↓ 5′---------ACTAGTTCTAGAGCGGCCGCCACCGCGGT---------3′ (SEQ.ID.N0.7) 3′---------TGATCAAGATCTCGCCGGCGGTGGCGCCA---------5′                              ↑                             

5′---------ACTAGTTCTAGAGC   GGCCGCCACCGCGGT---------3′ 3′---------TGATCAAGATCTCGCCGG   CGGTGGCGCCA---------5′

Example 6 Generation of Recombinant Molecules

Both the PCR amplified fragment (320 ng) and the linearized vector (600 ng) were incubated together in the presence of purified vaccinia DNA polymerase (150 ng) for 20 minutes as per the annealing assay described in the Materials and Methods. Reaction products were visualized by agarose electrophoresis (FIG. 8). Agarose gels showed that the majority of molecules formed under these conditions were the linear-dimers seen previously (FIG. 8, lane 5). However, because both ends of the PCR-amplified insert shared homology with the vector, a small portion of the reaction products were expected to, and did, migrate at positions characteristic of nicked-circular and higher concatemer forms (FIG. 8, lane 6). None of these reactions occurred in the presence of 5 μM dNTP (FIG. 8, lane 7).

Example 7 Transformation of Competent Cells

An aliquot (1-2 μL) of the reaction mixture from Example 6 was used to transform three different strains of E. coli (SURE, JM105 and DH5α) using standard procedures (SURE and DH5α, by electroporation and JM105, by heat shock). Appropriate dilutions were plated on LB+T plates containing 100 μg/mL ampicillin, 40 μg/mL X-gal (5-bromo-4-chloro-3-indolyl-β-D-galactoside), 0.5 mM IPTG (isopropylthio-β-galactoside) and 50 μg/mL thymine and incubated overnight at 37° C. DNA was isolated from transformed colonies and sequenced as described previously (Willer, McFadden and Evans, 1999

Table 1 shows data acquired using multiply-recombination deficient SURE cells, although all three strains gave similar results (0.5−2×10⁵ transformants per μg). White (W) colonies indicate transformation with potentially the correct construct. Blue (B) colonies indicate transformation with the vector substrate alone. It was clear that the yield of stable transformants was greatly dependent upon adding vaccinia DNA polymerase to the reaction mix. Recombinant (white) colonies were the most abundant product (83% of transformants in this particular experiment) even though the NotI-cut vector was not dephosphorylated. Thirteen putative recombinant plasmids were purified and it was observed that all 13 of the plasmids recovered from SURE cells were monomers incorporating a single DNA insert. DNA sequencing showed that all 13 molecules also encoded the insert in the correct orientation and at the expected position. There were 3 base substitutions located within one of the primer-binding sites and 2 other mutations within Taq polymerase-amplified DNA. The fusion points were those expected to be formed through annealing of homologous ends. It was concluded that the concatemers assembled by vaccinia virus polymerase can be processed into stable recombinants with a fidelity comparable to traditional cloning methods.

TABLE 1 Transformation of E. coli with recombinant joint molecules. Number of colonies Percent Transformants Reaction White Blue white per μg (×10⁻⁵) PCR-amplified insert (−) polymerase 2 0 100 N/A (+) polymerase 1 0 100 N/A Not1 restricted vector (−) polymerase 8 1,190 0.7 4.0 (+) polymerase 0 27 0.0 0.4 PCR-amplified insert plus Not1 restricted vector (−) polymerase 12 1,030 1.2 2.3 (+) polymerase 1,020 210 83 2.7 (+) polymerase, 7 220 3.1 0.5 (+) dNTP Joint molecules were prepared in reactions containing the indicated reaction components. E. coli SURE cells were electroporated with 1 μL of reaction products. The cells (100 μL or its equivalent) were plated and colonies were counted next day. Cell competency was estimated as 6 × 10¹⁰ transformants per μg using unrestricted pDW101.

Example 8 The Minimal Sequence Overlap

To determine the minimal amount of homology required for production of joint molecules, seven additional primer pairs were synthesized and then the set of eight oligonucleotide pairs were used to again PCR amplify a ˜800 bp fragment of SFV DNA. These 14 new PCR primers were similar in structure to the primers described above, except that the amount of sequence homologous to nucleotides flanking the NotI site in a NotI-cut vector now ranged from 4 to 18 bp. These substrates were incubated with vector DNA in optimized assays containing both vaccinia DNA polymerase and gpI3L, (which increased the ability to detect otherwise faint circular reaction products) and the yield of both linear and circular joint molecules were quantitated using densitometry. These and other experiments showed that as little as 10 bp of sequence homology between substrates still permitted strand joining by vaccinia polymerase, with a reaction optimum of about 14 bp (FIG. 9, panel B). These reaction products were also used to transform SURE cells, in triplicate, as there was some variation in the absolute efficiency of white transformant production from experiment to experiment. In all of the experiments, the percentage of white (recombinant) bacterial transformants closely paralleled the yield of joint molecules as detected by gel electrophoresis (FIG. 9A).

Example 9 Cloning a Recombinant Plasmid DNA with Vaccinia Virus DNA Polymerase

The method of the invention was successfully utilized to clone a recombinant DNA pRP406-SFV (FIG. 10, 11).

The cloning method of the present invention was compared with a traditional cloning method. Overall, the method of the present invention was simpler and quicker (Table 2).

Vector: pRP406 (SEQ. ID. NO. 8) was cut with PacI and BstEII and the larger fragment was purified to eliminate the smaller, intervening fragment.

Insert: PCR-SFV(˜800 bp, SEQ. ID. NO. 9), the polymerase chain reaction was used to amplify a fragment of Shope fibroma virus DNA. PCR primers added 16 bp sequences at the ends of the DNA that were homologous to sequences located at the ends of the cut vector (FIG. 10). Primers used when recombining DNA with pRP406 are shown in SEQ. ID. NOs. 10 and 11.

TABLE 2 Comparison of Cloning Strategies Joining by v DNA pol Traditional method with ligase PCR - With >12 nt homology with Cleaved with BstEII and Pac I amplified linear vector at both ends to generate the sticky ends insert 300 ng, 600 fmol 150 ng, 300 fmol Linear 250 ng, 100 fmol 100 ng, 40 fmol vector Reaction v pol 100 ng, v SSB 500 ng T4 DNA ligase 5 U in 10 ul condition in 20 ul 37° C. 10 min 20° C. 2 hr Trans- 1 of 20^(th) of reaction 1 of 10^(th) of reaction solution formation solution into E. coli SURE into E. coli SURE Recombinant 4.8 × 10⁴/ug vector 9.2 × 10⁴/ug vector frequency

While the present application has been described with reference to what are presently considered to be the preferred examples, it is to be understood that the invention is not limited to the disclosed examples. To the contrary, the invention is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.

All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.

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DETAILED LEGENDS FOR FIGURES

FIG. 1. DNA annealing catalyzed by vaccinia DNA polymerase. pDW101 was cut with EcoRI or XhoI to produce 2.96 kbp molecules sharing 33 bp of overlapping sequence homology (Panel A.). Annealing reactions (20 μL) were then prepared containing 0.35 μg of each DNA substrate plus 0.1 μg of vaccinia virus polymerase. After incubation for the indicated times, the reaction products were fractionated using agarose gel electrophoresis and visualized by ethidium bromide staining (Panel B). Alternatively, reactions were prepared containing 0.35 μg of each DNA substrate plus the indicated quantities of DNA polymerase and incubated for 20 min at 3T (Panel C.). A 6 kbp reaction product is formed in Panels B and C.

FIG. 2. Trimer formation. Panel A shows a schematic of the reaction. Note that joining three linear molecules is essentially the same reaction needed to join an insert DNA to the two flanking arms of a vector molecule. Panel B shows the reaction products analyzed on an ethidium-stained agarose gel. No joint molecules are formed when only one of the three substrates are provided to the polymerase. This shows that the reaction requires correct complementary sequences at the ends of the reacting molecules.

FIG. 3. Combinatorial fusion of DNA cassettes. In this simple scheme three different pools of DNA duplexes are prepared. Within a pool of molecules, the central portion of each molecule varies in sequence while the ends are identical. For example. A1-A5 all have the same ˜20 base sequence at the right end but the middle portions of these molecules vary in sequence. The left ends of molecules in the “B” pool are compatible with the right ends of molecules in the “A” pool. Similarly, the left ends of molecules in the “C” pool are compatible with the right ends of molecules in the “B” pool. Reaction with vaccinia polymerase will create trimers composed of one each of molecules selected from the “A”, “B”, and “C” pools. The resulting pool of trimers should express a random assortment of “A”, “B”, and “C” variants.

FIG. 4. Proposed cloning method. The PCR primers encode 10-20 additional nucleotides complementary to sequences flanking the vector insertion site.

FIG. 5. Substrate requirements. Reactions were prepared containing the indicated substrate DNAs plus or minus vaccinia DNA polymerase (0.1 μg) in 20 μL. The polymerase will not promote joint molecule formation unless two substrates are provided which share some overlapping end homology (lanes 1-6). When the DNA fragments can be differentiated by size, the reaction products comprise DNAs encoding the XhoI-EcoRI overlap region (lanes 8-13).

FIG. 6. Effect of vaccinia SSB (gpI3L) on joint molecule formation. Standard reactions (20 μL) contained 0.1 μg of vaccinia virus DNA polymerase (E) or 0.1 μg of polymerase plus 0.5 μg of vaccinia SSB (). The reactions were incubated for the indicated time, stopped, and the yield of joint molecules determined by gel electrophoresis (inset) and densitometry. Vaccinia SSB increased the extent of the reaction and stabilized the products.

FIG. 7. Trimer formation catalyzed by vaccinia virus DNA polymerase. Three substrates were prepared as indicated in the upper panel, and the middle substrate (“B”) labeled using polynucleotide kinase or Klenow polymerase. Reactions were prepared as indicated, incubated at 37° C. for 20 min. and then fractionated using agarose gel electrophoresis. The reaction products were first visualized with ethidium bromide, and then by autoradiography. No joint molecules were formed in reactions containing polymerase plus only a single DNA substrate (lanes 1 and 4). Only a 5′ label survived incubation with the polymerase and was incorporated into dimer and trimer molecules (lane 3).

FIG. 8. Cloning of PCR-amplified DNA using vaccinia virus DNA polymerase. An ˜800 hp PCR-amplified DNA fragment (“A”) was incubated with or without NotI-linearized pDW101 (“B”) and vaccinia virus DNA polymerase, as indicated.

The reaction products were separated by electrophoresis and visualized with ethidium bromide. Joint molecules were seen only in lane 6. Most of these joint molecules migrated at a position expected of linear dimers (lane 6), but a small portion of the reaction product migrated at a position typical of nicked circular molecules (arrowed). Adding 5 μM dNTPs blocked the reaction completely (lane 7). Table 1 summarizes the effect of transforming E. coli with these reaction products.

FIG. 9. Effect of homology length on joint molecule formation. PCR amplified DNAs were prepared containing 4, 6, 8, . . . , 18 bp of end sequence identical to sequences found flanking the NotI site in a pBluescript vector. A mixture of PCR amplified DNA plus NotI-cut vector was incubated with 0.1 μg of vaccinia DNA polymerase and 0.5 μg of gpI3L for 10 min and then separated by agarose gel electrophoresis (Panel B, inset). The yield of linear-duplex (

) and circular () joint molecules in each reaction was determined by densitometry (Panel B). Omitting the polymerase yielded no joint molecules (Δ). The reaction products (plus joint molecules prepared in two additional experiments) were used to transform bacterial SURE cells and the yield of recombinants determined as in Table 1 (Panel A).

FIG. 10 provides a map of DNA to be recombined to clone a recombinant DNA pRP4106-SFV using the method of the invention.

FIG. 11 shows the results of in vitro recombination of the linear DNA shown in FIG. 10 (shown on 0.8% agarose gel). After the joining reaction, 1 ul of reaction solution was used for transformation. The rest of solution was deproteinized and electrophoresized. 

1-30. (canceled)
 31. A kit for direct cloning of a linear DNA molecule comprising, in separate containers, a DNA polymerase and a reaction buffer, wherein the DNA polymerase has intrinsic exonuclease activity and is capable of performing a DNA joining reaction.
 32. The kit according to claim 31, further comprising a stimulatory factor.
 33. The kit according to claim 32, wherein the stimulatory factor is a single strand DNA binding protein.
 34. The kit according to claim 31, further comprising reagents to perform a positive control reaction.
 35. The kit according to claim 34, wherein the reagents to perform a positive control comprise a linearized vector, an insert DNA with first and second ends having appropriate complementary sequences, a DNA polymerase having intrinsic exonuclease activity that is capable of performing a DNA joining reaction, and a reaction buffer.
 36. The kit according to claim 35, wherein the reagents to perform a positive control further comprise a stimulatory factor.
 37. The kit according to claim 36, wherein the insert DNA is a PCR-amplified product.
 38. A DNA molecule prepared using a method of joining two or more linear DNA molecules comprising: obtaining two or more linear DNA molecules, each having an x and x′ strand having opposite polarities, wherein the 5′ end of the x′ strand of each linear DNA molecule has a sequence of nucleotides that is complementary to the 5′ end of the x strand of the linear DNA molecule to which it is to be joined; and incubating the two or more DNA molecules in the presence of a DNA polymerase under conditions whereby the two or more linear DNA molecules are joined; wherein the DNA polymerase has intrinsic exonuclease activity and joins the DNA molecules. 39-42. (canceled)
 43. A composition for cloning DNA molecules, comprising a carrier and DNA polymerase having exonuclease activity and capable of joining linear DNA molecules.
 44. A method of cloning DNA molecules comprising incubating DNA molecules in the presence of a DNA polymerase molecule having exonuclease activity and capable of joining DNA molecules.
 45. The method according to claim 44, wherein the DNA molecules are produced by PCR.
 46. The method according to claim 44, wherein the DNA polymerase comprises a polymerase selected from the group consisting of vaccinia virus DNA polymerase, T4 DNA polymerase and the Klenow fragment of E. coli. DNA polymerase I.
 47. A method of circularizing linear DNA molecules for site directed mutagenesis comprising: PCR amplifying a linear DNA molecule in the presence of primers that will introduce substantially complementary nucleic acid sequences onto each end of the linear DNA molecule; and incubating the PCR amplified linear DNA molecule in the presence of a DNA polymerase under conditions where the linear DNA molecule is circularized; wherein the DNA polymerase has intrinsic exonuclease activity and circularizes the DNA molecule. 